Correcting for bias in estimation of quantitative trait loci effects

Abstract -
Estimates of quantitative trait loci (QTL) effects
derived from complete genome scans are biased, if no assumptions are made
about the distribution of QTL effects. Bias should be reduced if estimates
are derived by maximum likelihood, with the QTL effects sampled from a known
distribution. The parameters of the distributions of QTL effects for nine
economic traits in dairy cattle were estimated from a daughter design
analysis of the Israeli Holstein population including 490 marker-by-sire
contrasts. A separate gamma distribution was derived for each trait.
Estimates for both the and parameters and their SE
decreased as a function of heritability. The maximum likelihood estimates
derived for the individual QTL effects using the gamma distributions for
each trait were regressed relative to the least squares estimates, but the
regression factor decreased as a function of the least squares estimate. On
simulated data, the mean of least squares estimates for effects with nominal
1% significance was more than twice the simulated values, while the mean
of the maximum likelihood estimates was slightly lower than the mean of the
simulated values. The coefficient of determination for the maximum
likelihood estimates was five-fold the corresponding value for the least
squares estimates.